2019-07-02T07:50:56 Created temporary directory: /tmp/pip-ephem-wheel-cache-k9dw339m
2019-07-02T07:50:56 Created temporary directory: /tmp/pip-req-tracker-hu_th_re
2019-07-02T07:50:56 Created requirements tracker '/tmp/pip-req-tracker-hu_th_re'
2019-07-02T07:50:56 Created temporary directory: /tmp/pip-wheel-8s5fzta1
2019-07-02T07:50:56 Collecting whatshap==0.11
2019-07-02T07:50:56   1 location(s) to search for versions of whatshap:
2019-07-02T07:50:56   * https://pypi.org/simple/whatshap/
2019-07-02T07:50:56   Getting page https://pypi.org/simple/whatshap/
2019-07-02T07:50:56   Analyzing links from page https://pypi.org/simple/whatshap/
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/35/95/43ff2304cd59ade39e64aadaeaec48e8c12bbe6262bcbbbd7b7d89487757/whatshap-0.9.tar.gz#sha256=beaadbc79e4d463b5e441b8e9a13b5345c07db3d91fb093cee1bfebfebae4442 (from https://pypi.org/simple/whatshap/), version: 0.9
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz#sha256=864d4ecfc33eac7265452f5a2f468a830779afc53e723119ecac5ecf73255acc (from https://pypi.org/simple/whatshap/), version: 0.10
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz#sha256=d0367a4dd0adf288d30a9a87b565e4f141745bec3ea825cb85ac3409a593bde9 (from https://pypi.org/simple/whatshap/), version: 0.11
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/01/84/31a5ea338647d0256a4a5c57e98d7a563f387e6a47f1e26299b89e3f2da1/whatshap-0.12.tar.gz#sha256=c65060155dc901e4d4bd48077706660e5b214540d4dc20575a8b2146fb6a11f9 (from https://pypi.org/simple/whatshap/), version: 0.12
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz#sha256=529646db74b2cac9f12ebd530bd7bb40cb073c367894bf66c5994c1d7f32b56a (from https://pypi.org/simple/whatshap/), version: 0.13
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/cd/d3/a63285d15b0da196a259197e46d9f61a852d1b3c94800f4a82ca4e31e307/whatshap-0.14.tar.gz#sha256=dd6076e67c5a4ce75d2510b3dbdd3c1e524124be62655f06c82f7d9fce4c5643 (from https://pypi.org/simple/whatshap/), version: 0.14
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/ec/d4/d6c19b716926895ee3def919ab23194212172ed5cf89ccb91c2949fb258d/whatshap-0.14.1.tar.gz#sha256=7b5781f1138b1830c4627451d1d5c77e7f2a3c5403510d9ab2a63f545911415b (from https://pypi.org/simple/whatshap/), version: 0.14.1
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz#sha256=2dc9d89d71cf99e10c71b6138edd456bfcf0d7355794bc3491078654df85bc38 (from https://pypi.org/simple/whatshap/), version: 0.15
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz#sha256=1df54d8705fb0451cc0a640918842481087f7b741778dfb4100cc1f4f60f48fe (from https://pypi.org/simple/whatshap/), version: 0.16
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/79/11/79da12b8c23f43b00fab8a6206f75cc1cc8c1902ff30eca53c17abe2f633/whatshap-0.17.tar.gz#sha256=8ad1c66789fe5fe957b3695902dae3c3fd4e67f79b9e349b92b532e9ff618933 (from https://pypi.org/simple/whatshap/), version: 0.17
2019-07-02T07:50:56     Skipping link https://files.pythonhosted.org/packages/97/19/5758de9357d2639e81f774dffd5227278df2df7f56e81f080098f00c8d5a/whatshap-0.18-cp34-cp34m-manylinux1_x86_64.whl#sha256=4a09adc24c6db3bd525667ac2559181dc94ee203a64f488dfce1ac38cbf44ba5 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4); it is not compatible with this Python
2019-07-02T07:50:56     Skipping link https://files.pythonhosted.org/packages/d0/72/94dc654f66164a351a1a9540e28b4bdf34a81046fbf26b5955725bea2f64/whatshap-0.18-cp35-cp35m-manylinux1_x86_64.whl#sha256=1c99980629655e58a34496b0e1b1c9123dddd0797a13cf681dcf83f92a6f33e0 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4); it is not compatible with this Python
2019-07-02T07:50:56     Skipping link https://files.pythonhosted.org/packages/0a/50/c9c89e7f3a59251a91e618165ccc2586b626643a4c59dfd8d1b32f9b6bbb/whatshap-0.18-cp36-cp36m-manylinux1_x86_64.whl#sha256=fdadadbed86cc7a7abd8f9ef3d55fe280eda957473db03dc30ad06ace6b877bd (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4); it is not compatible with this Python
2019-07-02T07:50:56     Skipping link https://files.pythonhosted.org/packages/32/77/e9e6f3e15a89ea87b0a3ed50e99af2a375a897707eb8b4c81209af918ff0/whatshap-0.18-cp37-cp37m-manylinux1_x86_64.whl#sha256=2e189cb51c2527444dada90f8fd2355ddfe8d9d35aca386330e63bc46c2d2699 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4); it is not compatible with this Python
2019-07-02T07:50:56     Found link https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4), version: 0.18
2019-07-02T07:50:56   Using version 0.11 (newest of versions: 0.11)
2019-07-02T07:50:56   Created temporary directory: /tmp/pip-unpack-m7epfwix
2019-07-02T07:50:56   Downloading https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz (309kB)
2019-07-02T07:50:56   Downloading from URL https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz#sha256=d0367a4dd0adf288d30a9a87b565e4f141745bec3ea825cb85ac3409a593bde9 (from https://pypi.org/simple/whatshap/)
2019-07-02T07:50:57   Added whatshap==0.11 from https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz#sha256=d0367a4dd0adf288d30a9a87b565e4f141745bec3ea825cb85ac3409a593bde9 to build tracker '/tmp/pip-req-tracker-hu_th_re'
2019-07-02T07:50:57     Running setup.py (path:/tmp/pip-wheel-8s5fzta1/whatshap/setup.py) egg_info for package whatshap
2019-07-02T07:50:57     Running command python setup.py egg_info
2019-07-02T07:50:58     running egg_info
2019-07-02T07:50:58     creating pip-egg-info/whatshap.egg-info
2019-07-02T07:50:58     writing pip-egg-info/whatshap.egg-info/PKG-INFO
2019-07-02T07:50:58     writing dependency_links to pip-egg-info/whatshap.egg-info/dependency_links.txt
2019-07-02T07:50:58     writing entry points to pip-egg-info/whatshap.egg-info/entry_points.txt
2019-07-02T07:50:58     writing requirements to pip-egg-info/whatshap.egg-info/requires.txt
2019-07-02T07:50:58     writing top-level names to pip-egg-info/whatshap.egg-info/top_level.txt
2019-07-02T07:50:58     writing manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt'
2019-07-02T07:50:59     reading manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt'
2019-07-02T07:50:59     writing manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt'
2019-07-02T07:50:59   Source in /tmp/pip-wheel-8s5fzta1/whatshap has version 0.11, which satisfies requirement whatshap==0.11 from https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz#sha256=d0367a4dd0adf288d30a9a87b565e4f141745bec3ea825cb85ac3409a593bde9
2019-07-02T07:50:59   Removed whatshap==0.11 from https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz#sha256=d0367a4dd0adf288d30a9a87b565e4f141745bec3ea825cb85ac3409a593bde9 from build tracker '/tmp/pip-req-tracker-hu_th_re'
2019-07-02T07:50:59 Building wheels for collected packages: whatshap
2019-07-02T07:50:59   Created temporary directory: /tmp/pip-wheel-gknjk745
2019-07-02T07:50:59   Building wheel for whatshap (setup.py): started
2019-07-02T07:50:59   Destination directory: /tmp/pip-wheel-gknjk745
2019-07-02T07:50:59   Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-8s5fzta1/whatshap/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-gknjk745
2019-07-02T07:51:00   running bdist_wheel
2019-07-02T07:51:00   running build
2019-07-02T07:51:00   running build_py
2019-07-02T07:51:00   creating build
2019-07-02T07:51:00   creating build/lib.linux-armv7l-3.7
2019-07-02T07:51:00   creating build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/graph.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/args.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/__main__.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/vcf.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/timer.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/bam.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/coverage.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/stats.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/verification.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/__init__.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/compare.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/variants.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:00   copying whatshap/phase.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:01   copying whatshap/example.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-02T07:51:01   running build_ext
2019-07-02T07:51:01   building 'whatshap.core' extension
2019-07-02T07:51:01   creating build/temp.linux-armv7l-3.7
2019-07-02T07:51:01   creating build/temp.linux-armv7l-3.7/whatshap
2019-07-02T07:51:01   creating build/temp.linux-armv7l-3.7/src
2019-07-02T07:51:01   arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c whatshap/core.cpp -o build/temp.linux-armv7l-3.7/whatshap/core.o -std=c++11
2019-07-02T07:51:04   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’:
2019-07-02T07:51:04   whatshap/core.cpp:6084:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2019-07-02T07:51:04      for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
2019-07-02T07:51:04                          ~~~~~~~~~~^~~~~~~~~~~
2019-07-02T07:51:04   whatshap/core.cpp: In function ‘std::vector<unsigned int> __pyx_convert_vector_from_py_unsigned_int(PyObject*)’:
2019-07-02T07:51:04   whatshap/core.cpp:11306:83: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-02T07:51:04        __pyx_t_5 = __Pyx_PyInt_As_unsigned_int(__pyx_v_item); if (unlikely(__pyx_t_5 == -1 && PyErr_Occurred())) __PYX_ERR(2, 52, __pyx_L1_error)
2019-07-02T07:51:04                                                                            ~~~~~~~~~~^~~~~
2019-07-02T07:51:04   whatshap/core.cpp:503:43: note: in definition of macro ‘unlikely’
2019-07-02T07:51:04      #define unlikely(x) __builtin_expect(!!(x), 0)
2019-07-02T07:51:04                                              ^
2019-07-02T07:51:05   whatshap/core.cpp: In function ‘void __Pyx__ExceptionSwap(PyThreadState*, PyObject**, PyObject**, PyObject**)’:
2019-07-02T07:51:05   whatshap/core.cpp:16039:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
2019-07-02T07:51:05        tmp_type = tstate->exc_type;
2019-07-02T07:51:05                           ^~~~~~~~
2019-07-02T07:51:05                           curexc_type
2019-07-02T07:51:05   whatshap/core.cpp:16040:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
2019-07-02T07:51:05        tmp_value = tstate->exc_value;
2019-07-02T07:51:05                            ^~~~~~~~~
2019-07-02T07:51:05                            curexc_value
2019-07-02T07:51:05   whatshap/core.cpp:16041:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
2019-07-02T07:51:05        tmp_tb = tstate->exc_traceback;
2019-07-02T07:51:05                         ^~~~~~~~~~~~~
2019-07-02T07:51:05                         curexc_traceback
2019-07-02T07:51:05   whatshap/core.cpp:16042:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
2019-07-02T07:51:05        tstate->exc_type = *type;
2019-07-02T07:51:05                ^~~~~~~~
2019-07-02T07:51:05                curexc_type
2019-07-02T07:51:05   whatshap/core.cpp:16043:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
2019-07-02T07:51:05        tstate->exc_value = *value;
2019-07-02T07:51:05                ^~~~~~~~~
2019-07-02T07:51:05                curexc_value
2019-07-02T07:51:05   whatshap/core.cpp:16044:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
2019-07-02T07:51:05        tstate->exc_traceback = *tb;
2019-07-02T07:51:05                ^~~~~~~~~~~~~
2019-07-02T07:51:05                curexc_traceback
2019-07-02T07:51:06   error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
2019-07-02T07:51:06   Building wheel for whatshap (setup.py): finished with status 'error'
2019-07-02T07:51:06   ERROR: Failed building wheel for whatshap
2019-07-02T07:51:06   Running setup.py clean for whatshap
2019-07-02T07:51:06   Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-8s5fzta1/whatshap/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2019-07-02T07:51:07   running clean
2019-07-02T07:51:07   removing 'build/temp.linux-armv7l-3.7' (and everything under it)
2019-07-02T07:51:07   removing 'build/lib.linux-armv7l-3.7' (and everything under it)
2019-07-02T07:51:07   'build/bdist.linux-armv7l' does not exist -- can't clean it
2019-07-02T07:51:07   'build/scripts-3.7' does not exist -- can't clean it
2019-07-02T07:51:07   removing 'build'
2019-07-02T07:51:07 Failed to build whatshap
2019-07-02T07:51:07 Cleaning up...
2019-07-02T07:51:07   Removing source in /tmp/pip-wheel-8s5fzta1/whatshap
2019-07-02T07:51:07 Removed build tracker '/tmp/pip-req-tracker-hu_th_re'
2019-07-02T07:51:07 ERROR: Failed to build one or more wheels
2019-07-02T07:51:07 Exception information:
2019-07-02T07:51:07 Traceback (most recent call last):
2019-07-02T07:51:07   File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 178, in main
2019-07-02T07:51:07     status = self.run(options, args)
2019-07-02T07:51:07   File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/commands/wheel.py", line 178, in run
2019-07-02T07:51:07     "Failed to build one or more wheels"
2019-07-02T07:51:07 pip._internal.exceptions.CommandError: Failed to build one or more wheels